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Yorodumi- PDB-1cf0: HUMAN PLATELET PROFILIN COMPLEXED WITH AN L-PRO10-IODOTYROSINE PEPTIDE -
+Open data
-Basic information
Entry | Database: PDB / ID: 1cf0 | ||||||
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Title | HUMAN PLATELET PROFILIN COMPLEXED WITH AN L-PRO10-IODOTYROSINE PEPTIDE | ||||||
Components |
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Keywords | COMPLEX (ACTIN-BINDING PROTEIN/PEPTIDE) / COMPLEX (ACTIN-BINDING PROTEIN-PEPTIDE) / PROFILIN / POLY-L-PROLINE / ACTIN CYTOSKELETON / COMPLEX (ACTIN-BINDING PROTEIN-PEPTIDE) complex | ||||||
Function / homology | Function and homology information synapse maturation / modification of postsynaptic actin cytoskeleton / negative regulation of actin filament bundle assembly / adenyl-nucleotide exchange factor activity / positive regulation of actin filament bundle assembly / negative regulation of actin filament polymerization / Signaling by ROBO receptors / regulation of actin filament polymerization / positive regulation of ATP-dependent activity / PCP/CE pathway ...synapse maturation / modification of postsynaptic actin cytoskeleton / negative regulation of actin filament bundle assembly / adenyl-nucleotide exchange factor activity / positive regulation of actin filament bundle assembly / negative regulation of actin filament polymerization / Signaling by ROBO receptors / regulation of actin filament polymerization / positive regulation of ATP-dependent activity / PCP/CE pathway / proline-rich region binding / positive regulation of ruffle assembly / negative regulation of stress fiber assembly / positive regulation of actin filament polymerization / positive regulation of epithelial cell migration / actin monomer binding / phosphatidylinositol-4,5-bisphosphate binding / phosphotyrosine residue binding / neural tube closure / RHO GTPases Activate Formins / modulation of chemical synaptic transmission / small GTPase binding / Platelet degranulation / actin binding / cell cortex / actin cytoskeleton organization / blood microparticle / cytoskeleton / protein stabilization / cadherin binding / focal adhesion / glutamatergic synapse / regulation of transcription by RNA polymerase II / RNA binding / extracellular exosome / membrane / nucleus / cytosol / cytoplasm Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / OTHER / Resolution: 2.2 Å | ||||||
Authors | Rozwarski, D.A. / Mahoney, N.M. / Almo, S.C. | ||||||
Citation | Journal: Nat.Struct.Biol. / Year: 1999 Title: Profilin binds proline-rich ligands in two distinct amide backbone orientations. Authors: Mahoney, N.M. / Rozwarski, D.A. / Fedorov, E. / Fedorov, A.A. / Almo, S.C. #1: Journal: Nat.Struct.Biol. / Year: 1997 Title: Structure of the Profilin-Poly-L-Proline Complex Involved in Morphogenesis and Cytoskeletal Regulation Authors: Mahoney, N.M. / Janmey, P.A. / Almo, S.C. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1cf0.cif.gz | 65.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1cf0.ent.gz | 49.3 KB | Display | PDB format |
PDBx/mmJSON format | 1cf0.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/cf/1cf0 ftp://data.pdbj.org/pub/pdb/validation_reports/cf/1cf0 | HTTPS FTP |
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-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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2 |
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS oper: (Code: given Matrix: (-0.935788, 0.199092, 0.29097), Vector: |
-Components
#1: Protein | Mass: 14868.945 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Tissue: PLATELET / Description: SYNTHETIC / Cellular location: CYTOPLASM / Plasmid: PMW172 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21 (DE3) / References: UniProt: P07737 #2: Protein/peptide | | Mass: 1084.003 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: The sequence occurs naturally in human #3: Water | ChemComp-HOH / | Nonpolymer details | RESIDUE 11 OF CHAIN E REPRESENTS AN IODOTYROSINE RESIDUE CONNECTED BY A PEPTIDE BOND TO THE POLY- ...RESIDUE 11 OF CHAIN E REPRESENTS | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.2 Å3/Da / Density % sol: 42 % |
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Crystal grow | pH: 8 / Details: pH 8.0 |
Crystal grow | *PLUS Method: other / Details: Mahoney, N.M., (1997) Nat.Struct.Biol., 4, 953. |
-Data collection
Diffraction | Mean temperature: 298 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418 |
Detector | Type: SIEMENS X1000 / Detector: AREA DETECTOR / Date: May 1, 1996 / Details: MIRRORS |
Radiation | Monochromator: GRAPHITE CRYSTAL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2.2→20 Å / Num. obs: 17247 / % possible obs: 95.2 % / Redundancy: 3 % / Rmerge(I) obs: 0.62 / Rsym value: 0.62 |
Reflection | *PLUS Rmerge(I) obs: 0.062 |
-Processing
Software |
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Refinement | Method to determine structure: OTHER / Resolution: 2.2→8 Å / Data cutoff high absF: 1000000 / Data cutoff low absF: 0.001 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 2 Details: WATER MOLECULES 201 - 214 INTERACT WITH PROTEIN CHAIN A WATER MOLECULES 301 - 314 INTERACT WITH PROTEIN CHAIN B AND EACH SET OF WATER MOLECULES ARE RELATED BY THE SAME NCS SYMMETRY THAT ...Details: WATER MOLECULES 201 - 214 INTERACT WITH PROTEIN CHAIN A WATER MOLECULES 301 - 314 INTERACT WITH PROTEIN CHAIN B AND EACH SET OF WATER MOLECULES ARE RELATED BY THE SAME NCS SYMMETRY THAT RELATES THE TWO PROTEIN CHAINS
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Displacement parameters | Biso mean: 25.6 Å2
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Refinement step | Cycle: LAST / Resolution: 2.2→8 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.2→2.28 Å / Total num. of bins used: 10
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Xplor file |
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Refinement | *PLUS % reflection Rfree: 10 % / Rfactor Rfree: 0.31 / Rfactor Rwork: 0.21 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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LS refinement shell | *PLUS Rfactor Rfree: 0.398 / Rfactor Rwork: 0.336 |